49,320 research outputs found
Aligning Multiple Sequences with Genetic Algorithm
The alignment of biological sequences is a crucial
tool in molecular biology and genome analysis. It helps to build
a phylogenetic tree of related DNA sequences and also to predict
the function and structure of unknown protein sequences by
aligning with other sequences whose function and structure is
already known. However, finding an optimal multiple sequence
alignment takes time and space exponential with the length or
number of sequences increases. Genetic Algorithms (GAs) are
strategies of random searching that optimize an objective
function which is a measure of alignment quality (distance) and
has the ability for exploratory search through the solution space
and exploitation of current results
Cheating for Problem Solving: A Genetic Algorithm with Social Interactions
We propose a variation of the standard genetic algorithm that incorporates
social interaction between the individuals in the population. Our goal is to
understand the evolutionary role of social systems and its possible application
as a non-genetic new step in evolutionary algorithms. In biological
populations, ie animals, even human beings and microorganisms, social
interactions often affect the fitness of individuals. It is conceivable that
the perturbation of the fitness via social interactions is an evolutionary
strategy to avoid trapping into local optimum, thus avoiding a fast convergence
of the population. We model the social interactions according to Game Theory.
The population is, therefore, composed by cooperator and defector individuals
whose interactions produce payoffs according to well known game models
(prisoner's dilemma, chicken game, and others). Our results on Knapsack
problems show, for some game models, a significant performance improvement as
compared to a standard genetic algorithm.Comment: 7 pages, 5 Figures, 5 Tables, Proceedings of Genetic and Evolutionary
Computation Conference (GECCO 2009), Montreal, Canad
Signatures of arithmetic simplicity in metabolic network architecture
Metabolic networks perform some of the most fundamental functions in living
cells, including energy transduction and building block biosynthesis. While
these are the best characterized networks in living systems, understanding
their evolutionary history and complex wiring constitutes one of the most
fascinating open questions in biology, intimately related to the enigma of
life's origin itself. Is the evolution of metabolism subject to general
principles, beyond the unpredictable accumulation of multiple historical
accidents? Here we search for such principles by applying to an artificial
chemical universe some of the methodologies developed for the study of genome
scale models of cellular metabolism. In particular, we use metabolic flux
constraint-based models to exhaustively search for artificial chemistry
pathways that can optimally perform an array of elementary metabolic functions.
Despite the simplicity of the model employed, we find that the ensuing pathways
display a surprisingly rich set of properties, including the existence of
autocatalytic cycles and hierarchical modules, the appearance of universally
preferable metabolites and reactions, and a logarithmic trend of pathway length
as a function of input/output molecule size. Some of these properties can be
derived analytically, borrowing methods previously used in cryptography. In
addition, by mapping biochemical networks onto a simplified carbon atom
reaction backbone, we find that several of the properties predicted by the
artificial chemistry model hold for real metabolic networks. These findings
suggest that optimality principles and arithmetic simplicity might lie beneath
some aspects of biochemical complexity
Embodied Evolution in Collective Robotics: A Review
This paper provides an overview of evolutionary robotics techniques applied
to on-line distributed evolution for robot collectives -- namely, embodied
evolution. It provides a definition of embodied evolution as well as a thorough
description of the underlying concepts and mechanisms. The paper also presents
a comprehensive summary of research published in the field since its inception
(1999-2017), providing various perspectives to identify the major trends. In
particular, we identify a shift from considering embodied evolution as a
parallel search method within small robot collectives (fewer than 10 robots) to
embodied evolution as an on-line distributed learning method for designing
collective behaviours in swarm-like collectives. The paper concludes with a
discussion of applications and open questions, providing a milestone for past
and an inspiration for future research.Comment: 23 pages, 1 figure, 1 tabl
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